Thursday, May 20, 2010

This blog has been hosting a sporadicseries interviewing the editors from various open access journals for paleontologists. This time around, I am very pleased to highlight Palaeontologia Electronica (PE for short). PE has a special place in my heart for two reasons. First, it was the earliest open access paleo journal around (that I know of). It began publication in 1998, before "open access" was even a part of the scientific vocabulary! Second, one of my first peer reviewed publications graced the pages of the journal, back in 2004.

PE's executive editor, P. David Polly, was kind enough to answer a few questions. As is only fair, he has asked me to remind readers that any opinions stated here are his alone, and do not necessarily represent official views of the journal.

How did you get involved with PE?I got involved with PE in 1996, just after its inception and before the first issue was published. As I recall, the idea of an electronic journal of paleontology had been the idea of Norman MacLeod, Tim Patterson, and William Riedel in 1995, who then enthused the group of people who made up the first editorial board. Mark Purnell, my co-executive editor, Peter Roopnarine, the special issue editor, and Jennifer Rumford, our production editor, were all part of that group. So there are four of us who have been with PE for more than 14 years.

Given your long history with PE, have there been any particular surprises for you in how the journal has developed?The main surprise was how hard it was to get people to publish with PE in the early days. Younger scientists were the ones most attracted by the idea, but they were also the ones to whom "impact factors" were the most important. The journal wasn't indexed by Thomson-Reuters until a few years ago and has only had an official "impact factor" since 2007. Before then we often struggled to get enough submissions to fill an issue, but since then the number of papers that come in is similar (or greater) than many other paleo journals.

Within the growing ecosystem of open access journals, what makes PE unique?PE is unique in that it is completely sponsored by professional societies so that neither readers nor authors have to pay. Many so-called "open access" journals allow readers to have free access, but charge authors a steep fee. In my opinion, that funding model is even worse than high subscription fees for readers because funds for publication are not equally distributed among fields (paleo as a field has far few funds available for publication costs than does, say, medicine), nor are they equally distributed among researchers, institutions, or countries within a field. Publication is a fundamental part of science, or any academic discipline for that matter-- it's imperative that reserachers be able to publish their work and that others be able to read it.

In my mind, it is an obligation for anyone involved in a professional academic field to donate their time to reviewing papers, serving on editorial boards, paying dues to professional societies, and working for those societies to help facilitate and subsidize scientific publication. Sadly it is becoming increasingly difficult to get people to review papers, serve as editors, or otherwise commit time to these activities, which increasingly leaves academic publishing in the hands of corporate publishers, much to the detriment of fields like paleontology. No service that is offered by corporate publishing houses couldn't be offered by the academic community. The goal of PE is to publish quality science at the least possible cost, without taking a profit, and to reach the greatest possible audience.

What advice would you give to authors interested in submitting their research to the journal?Format their papers correctly and, regardless of whether you submit to PE or another journal, to be willing to review at least five papers for every one you publish.

Are there any myths about PE that you'd like to see busted?The main myth about PE that should be busted is that publication is instant. Once papers are accepted to PE, they come out in the next issue, which is faster than most journals, but the process of review and revision happens at the same speed as for any other paper. The thing that slows papers down the most is finding reviewers. I probably have two or three people decline to review for every one who says yes.... it can sometimes take a couple of months to find two suitable reviews for a paper. But once reviews have been found, revisions have been made, and proper formatting done, the papers come out quickly in PE.

Thursday, May 6, 2010

Yesterday, I ran the first part of this two-part interview with Anthony (Tony) Martin, senior author on a new paper in PLoS ONE. The research details a rare trace fossil (figured below) left behind by a bottom-feeding fish over 50 million years ago. Yesterday's questions focused on the science - in the final installment, we'll learn more about the publishing process. (Full disclosure: I am an editor for PLoS ONE, and was the editor who handled this manuscript.)

Why did you choose PLoS ONE as a venue for the manuscript?All three of us really liked the fact that by publishing in PLoS ONE we could better share our research with both our colleagues and the general public. All too often I’ve published papers that were read by maybe two or three dozen of my colleagues (if I’m lucky), rather than a broader audience that might also find the work really interesting. I’ve also published in journals with “pay walls” erected to prevent non-subscribers from seeing articles. I know this really frustrates some science bloggers who want to write about the original research instead of just relying on press releases or news articles. So I am becoming more enamored with making sure all science enthusiasts have free access to original research results. PLoS ONE also has published some top-notch paleontological articles in the past few years, so it’s become a high-profile place to publish, while also permitting laypeople to learn from our science.

We also thought this research made for an interesting “fish story” combined with a “detective story,” sort of Sherlock Holmes-meets-fishing-meets-paleontology-meets-spatial analysis. The study also has some visually interesting elements, which through publishing in an electronic journal we could better share through our new (and very cool) application of the Deep Zoom™ software (link here). Now anyone with an Internet connection can check out the same trace fossil analyzed in the study through the pan-and-zoom function of the software.

Was there anything about the PLoS ONE process (good or bad) that surprised you?Not really. One of my coauthors, Gonzalo [Vazquez-Prokopec] had previouslypublished in one of the PLoS journals and said it was a straightforward process, with timely peer review and good, thorough feedback from the reviewers and editors. I’m pleased to say that our experience was the same, and it encourages me to consider PLoS ONE for future contributions.

Which of the Green River fish would have tasted best?I would have loved to try Priscacara liops, either pan-fried or steamed with ginger, garlic, scallions, and soy. I’m not so sure that Notogoneus osculus [the focus of the current paper] would have been nearly as tasty, especially considering that we’re even more certain now it was a bottom feeder.

A big thank you to Tony, for taking the time for this interview. Don't forget to check out the paper, if you haven't already!

Wednesday, May 5, 2010

The open access journal PLoS ONE has published a lot of neat paleontology articles over the last few years (see here for a reasonably comprehensive listing). Charismatic, terrestrial vertebrates (whether dinosaurs, Ice Age mammals, or prehistoric humans) seem to dominate. But what about the poor, neglected fish?

Today, PLoS ONE published a nifty article by Anthony (Tony) Martin [pictured at left] and colleagues, discussing a 50 million year old fish feeding and swimming trace fossil from Wyoming. In the build-up to the release of their paper, Tony (a paleontologist with a specialization in trace fossils, over at Emory University) was kind enough to answer a few questions about the paper. Part 1 (focusing on the science behind the paper) is posted today, and Part 2 (focusing on the open access angle) will arrive tomorrow. [Full disclosure: I was the academic editor at PLoS ONE who handled this submission]

Briefly, what is the importance of the finding described in your new paper?

Several parts of it are important, and they’re all related.

One is that this is the first fish trace fossil described in detail from a formation that’s world-famous for its fish body fossils, the Green River Formation near Kemmerer, Wyoming. The Green River Formation was made by a series of lakes about 50 million years ago, and it preserved many gorgeous fossil fish, which have been collected and studied since the 1850s. However, fish trace fossils, such as trails made by their fins while swimming along the lake bottom, have been mostly neglected. Trace fossils can be extremely valuable for directly reflecting ancient behavior, and because the trace fossil we studied was extraordinarily detailed, it gave us some new insights we might not have gleaned from the fish body fossils.

Secondly, we are very sure about the species of fish made the trace fossil, namely, Notogoneus osculus[figured at right]. This fish had always been interpreted as a bottom feeder, and this is the first trace fossil to confirm this behavior. Our identification of the tracemaker is unusual, because oftentimes it’s tough to tell just what animal made a particular trace fossil. This one, though, gave us some great clues about “who done it.” The trace fossil [see figure below] has beautiful sine-like waves and other marks that show it made by a fish with a downward-pointing mouth, two pelvic pins, an anal fin, and a caudal fin. What really cinched it, though, was that this same species is also found as a body fossil in the same layer as the trace fossil. So our conclusion about the tracemaker is a pretty tight fit in every respect.

Thirdly, we figured out the size of the fish by applying some mathematical and spatial-analysis techniques that had never been used previously on a fish trace fossil. From these methods, we were calculated that the fish was 45 cm, or about 18 inches, which is exactly the average size of Notogoneus osculus. So not only do we know which fish did it, we know how big it was! This makes for a great fish story, because we can say that it was “the one that got away,” we can tell people what it was, and hold out our hands to say, “and it was THIS big (45 cm).” The kicker, of course, is that we’re talking about a fish from 50 million years ago, and in a lake that dried up nearly that long ago.

Lastly, this trace fossil shows a fish behaving normally, swimming and feeding along the lake bottom. Yet it was made in the deepest part of Fossil Lake, which supposedly excluded live fish because of low-oxygen conditions. So this fish trace fossil, along with a few others we mention in the paper, should give future researchers a good reason to reconsider the paleoecology of Fossil Lake. We now know that fish feeding on the bottom of the deepest part of Fossil Lake was a part of its benthic ecology, giving us a new insight about this long-studied deposit.

If you could share one thing about the research that didn't make it into the paper, what would that be? Is there an interesting back story to the project?

Actually, two things should be mentioned, the back story and a philosophical perspective.

The back story is that this may be the only paleontological paper in which the coauthors consist of an ichnologist (me), a disease ecologist (Gonzalo Vazquez-Prokopec), and a geographer (Michael Page). I know it sounds like the start of a bad (and really nerdy) joke, as in, “An ichnologist, a disease ecologist, and a geographer walked into a bar one day…”, but it was a great opportunity for the three of us, all in the same Environmental Studies department at Emory University, to work together in a creative and synergistic way. I did the primary detective work, interpreting the trace fossil in the broadest sense, Gonzalo did some spatial analysis and Fourier transform calculations, and Michael put together the Deep Zoom™ application that allows a viewer to look at a detailed digital image of the trace fossil. This shows how science can work in imaginative ways!

The philosophical point I want to make is summarized by a sentence buried in the paper that refers to places where the fish’s fins lifted off the bottom of the lake and left no marks:

“In other words, these breaks in the continuity of the fin trails also constitute parts of the trace fossil, and have behavioral significance.”

A metaphor I will use to describe this is that the moments of silence in a piece of music are also part of the music. Likewise in this trace fossil, wherever the fish did not touch the bottom, these “empty” places are still part of the trace fossil, and filled with meaning.

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Ramblings on the role of open source software and open access publishing in paleontology, the latest and sometimes not-so-greatest ways in which we reconstruct the past, and the occasional bits of career advice and paleo news.

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This is a personal weblog, and the opinions expressed here represent my own and not those of my employer or any other organization with which I am associated. Although I strive for accurate information, please be aware that the advice offered here is "as is," with no claims or guarantees that it will work for you. Hey, I'm just a paleontologist.